We have made a detailed study of the X-chromosome replication pattern during the period when X-inactivation is occurring in the mouse embryo. Our observations show unequivocal regionalization of the embryo with respect to the temporal X-chromosome. The switch from isocyclic to allocyclic replication occurs in the embryonic ectoderm at approximately 6 days of development and is random with respect to parental origin of the X-chromosome. In the extra-embryonic tissues, however, the switch to allocyclic replication has apparently occurred prior to 5.3 days of development and almost exclusively involves the paternally-derived X-chromosome. Since these findings are consistent with results obtained in biochemical studies of X-chromosome activity in female embryos, we conclude that there is a close temporal relationship between the cytogenetic and biochemical manifestations of the X-inactivation process. In addition, we have observed a pattern of early paternal X-chromosome replication, transitory in some cases, that is unique to extra-embryonic tissues. These results suggest that there may be some differences in the mechanism by which X-inactivation occurs in the extra-embryonic tissues as compared with the embryonic ectoderm.